rs753420

Variant names:

• chr19-36152793-T-G
• rs753420
• ENST00000721182.1:n.38+1271T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000721182.1(ENSG00000294115):​n.38+1271T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 212,566 control chromosomes in the GnomAD database, including 10,591 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.29 (7066 hom., cov: 32)
  • Exomes 𝑓: 0.33 (3525 hom.)
• Consequence: ENSG00000294115 ENST00000721182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 24 publications found

Genes affected

ENSG00000294115 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294115	ENST00000721182.1	n.38+1271T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44606 AN: 151976 Hom.: 7052 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.326 AC: 19703 AN: 60472 Hom.: 3525 Cov.: 0 AF XY: 0.324 AC XY: 9807 AN XY: 30266

African (AFR) AF: 0.277 AC: 646 AN: 2330

American (AMR) AF: 0.413 AC: 717 AN: 1736

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 781 AN: 2628

East Asian (EAS) AF: 0.659 AC: 3481 AN: 5286

South Asian (SAS) AF: 0.414 AC: 221 AN: 534

European-Finnish (FIN) AF: 0.284 AC: 1010 AN: 3560

Middle Eastern (MID) AF: 0.297 AC: 107 AN: 360

European-Non Finnish (NFE) AF: 0.286 AC: 11339 AN: 39600

Other (OTH) AF: 0.316 AC: 1401 AN: 4438

GnomAD4 genome AF: 0.294 AC: 44663 AN: 152094 Hom.: 7066 Cov.: 32 AF XY: 0.296 AC XY: 22007 AN XY: 74342

African (AFR) AF: 0.268 AC: 11102 AN: 41492

American (AMR) AF: 0.355 AC: 5428 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3472

East Asian (EAS) AF: 0.659 AC: 3401 AN: 5164

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4816

European-Finnish (FIN) AF: 0.257 AC: 2713 AN: 10574

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18440 AN: 67972

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.285 Hom.: 25966

Bravo AF: 0.303

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.49
PhyloP100		0.059
PromoterAI		0.035	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs753420; hg19: chr19-36643695; COSMIC: COSV53084711; COSMIC: COSV53084711;